Xrn1 is a deNADding enzyme modulating mitochondrial NAD-capped RNA

Sunny Sharma,Jun Yang,Ewa Grudzien-Nogalska,Kelvin Y Kwan,Megerditch Kiledjian,Jessica Shivas

doi:10.1038/s41467-022-28555-7

Sunny Sharma, Jun Yang + Show 4 more

Open Access

https://doi.org/10.1038/s41467-022-28555-7

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Abstract

The existence of non-canonical nicotinamide adenine diphosphate (NAD) 5′-end capped RNAs is now well established. Nevertheless, the biological function of this nucleotide metabolite cap remains elusive. Here, we show that the yeast Saccharomyces cerevisiae cytoplasmic 5′-end exoribonuclease Xrn1 is also a NAD cap decapping (deNADding) enzyme that releases intact NAD and subsequently degrades the RNA. The significance of Xrn1 deNADding is evident in a deNADding deficient Xrn1 mutant that predominantly still retains its 5′-monophosphate exonuclease activity. This mutant reveals Xrn1 deNADding is necessary for normal growth on non-fermenting sugar and is involved in modulating mitochondrial NAD-capped RNA levels and may influence intramitochondrial NAD levels. Our findings uncover a contribution of mitochondrial NAD-capped RNAs in overall NAD regulation with the deNADding activity of Xrn1 fulfilling a central role.

Highlights

The existence of non-canonical nicotinamide adenine diphosphate (NAD) 5′-end capped RNAs is well established
Detection of an NAD cap on post-transcriptionally processed intronic small nucleolar RNAs in mammalian cells has advocated the existence of a post-transcriptional NAD-capping mechanism as well[3]
NAD caps are found on certain regulatory RNAs2, while in budding yeast Saccharomyces cerevisiae, they are on a subset of mitochondrial RNAs and transcripts encoding the translational machinery[4]

Summary

Introduction

The existence of non-canonical nicotinamide adenine diphosphate (NAD) 5′-end capped RNAs is well established. The significance of Xrn[1] deNADding is evident in a deNADding deficient Xrn[1] mutant that predominantly still retains its 5′-monophosphate exonuclease activity This mutant reveals Xrn[1] deNADding is necessary for normal growth on non-fermenting sugar and is involved in modulating mitochondrial NAD-capped RNA levels and may influence intramitochondrial NAD levels. Detection of an NAD cap on post-transcriptionally processed intronic small nucleolar RNAs (snoRNAs) in mammalian cells has advocated the existence of a post-transcriptional NAD-capping mechanism as well[3]. These studies have led to the identification of a battery of NAD-cap decapping (deNADding) enzymes—NudC in bacteria[2,7,8] and its human homolog Nudt[129,10], Nudt1610 and the DXO/Rai[1] family of non-canonical decapping enzymes[3,11]. Despite the occurrence of NAD caps in diverse organisms, the biological role of this non-canonical metabolite cap in cellular physiology has remained elusive

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